Interconnection networks for parallel molecular dynamics simulation based on hamiltonian cubic symmetric topology |
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Authors: | Klavdija Kutnar Urban Bor?tnik Dragan Maru?i? Du?anka Jane?i? |
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Institution: | (1) University of Primorska, FAMNIT, Glagoljaška 8, 6000 Koper, Slovenia;(2) National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia;(3) IMFM, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia |
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Abstract: | A class of interconnection networks for efficient parallel MD simulations based on hamiltonian cubic symmetric graphs is presented.
The cubic symmetric graphs have many desirable properties as interconnection networks since they have a low degree and are
vertex- and edge-transitive. We present a method for scheduling collective communication routines that are used in parallel
MD and are based on the property that the graphs in question have a Hamilton cycle, that is, a cycle going through all vertices
of the graph. Analyzing these communication routines shows that hamiltonian cubic symmetric graphs of small diameter are good
candidates for a topology that gives rise to an interconnection network with excellent properties, allowing faster communication
and thus speeding up parallel MD simulation. |
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Keywords: | Cubic symmetric graphs Interconnection networks Communication scheduling |
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